http://www.ft86club.com/files/BRZwiringi.pdf
Page 109 clearly shows the wiring of the cruise control main switch. Since there's only two wires, I'm guessing there is a specific amount of voltage drop or signals that tell the car of each setting for cruise purposes.
My guess at this point is a malfunctioning cruise control main switch, assuming the ECU is properly flashed with no CEL. CEL will actually result in the cruise light on the dash being constant yellow instead of green.
-alex